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rvaser / spoa

SIMD partial order alignment tool/library
MIT License
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How to get both GFA and MSA as output? #51

Closed AndreaGuarracino closed 3 years ago

AndreaGuarracino commented 3 years ago

Hi @rvaser,

is it possible to obtain as output in a single run both the partial order graph (GFA) and the multiple sequence alignment (FASTA)?

rvaser commented 3 years ago

Hi Andrea, at this point no. I'll figure out a way how to enable it, but in 2 weeks or so.

Best regards, Robert

rvaser commented 3 years ago

I forgot about this issue, sorry. Would it be acceptable to print the GFA first, followed by an empty line, and then the FASTA (both to stdout)? Or without the new line, the FASTA can be distinguished by > at the beginning of line.

AndreaGuarracino commented 3 years ago

Hi Robert,

I think it would work because we users should just add a shell/convenient way to separate the two parts on the fly into two different files. Thank you!

rvaser commented 3 years ago

I enabled multiple -r options so you can mix and match different output formats as you like. E.g. you can now run spoa as spoa -r 0 -r 1 -r 0 reads.fa and you will get consensus, msa, consensus as output.

AndreaGuarracino commented 3 years ago

Nice, it is very general! I would suggest editing the documentation, because now, for example, -r1 -r0 is very similar to -r2, but in the first case the consensus is without gaps (and its header is slightly different). However, it works well, thank you! Now I want #31. Push, push, push! :P